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#ifndef SEQUENCEPARSER_H
#define SEQUENCEPARSER_H
/*
* sequenceParser.h
* Mothur
*
* Created by westcott on 9/9/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "utils.hpp"
#include "mothurout.h"
#include "sequence.hpp"
#include "groupmap.h"
#include "splitgroupscommand.h"
/* This class reads a fasta and group file with a namesfile as optional and parses the data by group.
Note: The sum of all the groups unique sequences will be larger than the original number of unique sequences.
This is because when we parse the name file we make a unique for each group instead of 1 unique for all
groups.
*/
class SequenceParser {
public:
SequenceParser(string, string, vector<string>); //group, fasta, groups (if blanks then all) - file mismatches will set m->setControl_pressed(true)
SequenceParser(string, string, string, vector<string>); //group, fasta, name, groups (if blanks then all) - file mismatches will set m->setControl_pressed(true)
~SequenceParser();
//general operations
int getNumGroups();
vector<string> getNamesOfGroups();
vector<string> getFiles(string); //returns fasta and count file a specific group.
map<string, vector<string> > getFiles() { return groupToFiles; } //returns all files groupName - > vector of groups files (fasta, optionalName, group);
private:
MothurOut* m;
Utils util;
bool hasName;
map<string, vector<string> > groupToFiles; //groupName -> fasta, name, group or groupName -> fasta, group
vector<string> namesOfGroups; //namesOfGroups in same order as groupToSeqs;
};
#endif
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